I've had trouble with MySQL dying in the wee hours of the morning. Today, it was 5:41am. When I checked the processes, there were 56 locked processes tied to my problem Threads database. I have repaired and optimized this database in the last week or two, but the problem persists. I have another instance of Threads on this server, but it's less-active database did NOT show any locked processes.
I've been told that MySQL can become zombie if there are a lot of locked processes - that sounds like my problem.